Muddies don't just feed head down.
Perch yourself on a high spot, you will see muddies on their sides, pectoral fins poking out the water as they scour the sides and undersides of rocks. You can often see the round circular depressions their mouthes make on the algae on the rocks.
More likely than not it is to do with timing and not with how the fish feed, I've seen yellows feeding facing downstream too. You have to remember a muddy has it's eyes more or less on the top of the head and their mouth is underslung, so between the time they see something yummy and swipe at it to suck it in there is always a delay. With a naturally drifting nymph or caddis, this would mean the item being swiped at would stick around for a little longer due to the turbulence created by their movement allowing them to suck it in, unlike your flies which are weighted and keep on moving along chasing your line and indicator, which are again moving at a different speed than the food in the bottom layer of water so with the delay between you seeing the take to and striking, the fly has moved further on, and as the accelerating fly will hook into the first thing that offers resistance, you hook the muddy in the arse or the dorsal fin.
Follow the advice given, dump the indicators, muddies more often than not NAIL the fly they're taking and don't discriminate against the muddies. They make for GREAT fun when the SmallMouth aren't playing along and are by no means an inferior species to target.
My R0.02.
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